<PAGE>   1
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
   
                                  FORM 10-K/A
    
     [X] ANNUAL REPORT PURSUANT TO SECTION 13 OR 15 (d) OF THE SECURITIES
EXCHANGE ACT OF 1934

For the fiscal year ended September 30, 1998
                                       or

     [ ] TRANSITION REPORT PURSUANT TO SECTION 13 OR 15 (d) OF THE SECURITIES
EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM ________ to ________

                          Commission File No. 0-18728


                        INTERNEURON PHARMACEUTICALS, INC.
              (Exact name of registrant as specified in its charter)


         Delaware                                              04-3047911
(State or other jurisdiction of                             (I.R.S. Employer
incorporation or organization)                           Identification Number)

One Ledgemont Center, 99 Hayden Avenue, Lexington, MA             02421
(Address of principal executive offices)                       (Zip Code)


Registrant's telephone number, including area code:  (781) 861-8444

Securities registered pursuant to Section 12(b) of the Act: None

Securities registered pursuant to Section 12(g) of the Act: Common Stock, $.001
par value

Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding twelve (12) months (or for such shorter period that
the registrant was required to file such report(s)), and (2) has been subject
to the filing requirements for the past ninety (90) days.         YES [X] NO

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405
of Regulation S-K is not contained herein, and will not be contained, to the
best of registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K [X].

The aggregate market value of the voting and non-voting common equity (excluding
preferred stock convertible into and having voting rights on certain matters
equivalent to 622,222 shares of common stock) held by non-affiliates of the
registrant was approximately $69,500,000, based on the last sales price of the
Common Stock as of December 21, 1998. Shares of Common Stock held by each
executive officer and director, by each person who beneficially owns 10% or more
of the outstanding common stock, and individuals or entities related to such
persons have been excluded. This determination of affiliate status may not be
conclusive for other purposes.

As of December 21, 1998, 41,817,017 shares of Common Stock, $.001 par value, of
the registrant were issued and outstanding.

                      DOCUMENTS INCORPORATED BY REFERENCE

See Part III hereof with respect to incorporation by reference from the
registrant's definitive proxy statement for the fiscal year ended September 30,
1998 to be filed pursuant to Regulation 14A under the Securities Exchange Act of
1934 and the Exhibit Index hereto.


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     Item 6. Selected Financial Data

     The selected financial data presented below summarizes certain financial
data which has been derived from and should be read in conjunction with the more
detailed consolidated financial statements of the Company and the notes thereto
which have been audited by PricewaterhouseCoopers LLP, independent accountants,
whose report thereon is included elsewhere in this Annual Report on Form 10-K
along with said financial statements. See "Management's Discussion and Analysis
of Financial Condition and Results of Operations".
<TABLE>
<CAPTION>

                                                                        Fiscal Years Ended September 30,
                                                                  (Amounts in thousands except per share data)     
                                                              1994        1995       1996         1997        1998
                                                          --------    --------    -------     --------    --------
<S>                                                      <C>         <C>        <C>          <C>          <C>      
STATEMENT OF OPERATIONS DATA:                                                                                      
Product revenue ........................................  $     --    $     --    $ 13,779    $ 55,945    $     -- 
Contract and license fee revenue .......................       101       3,463       8,335      11,039       6,488 
Total revenues .........................................       101       3,463      22,114      66,984       6,488 

Cost of product revenue ................................        --          --      11,454      41,144          -- 
Research and development ...............................    17,737      15,070      17,344      50,180      39,762 
Selling, general and administrative ....................     8,341       7,142      13,991      19,581      21,975 
Product withdrawal .....................................        --          --          --       7,528          -- 
Purchase of in-process research and development ........     1,852          --       6,434       3,044         500 

Net loss from operations ...............................   (27,829)    (18,749)    (27,109)    (54,493)    (55,749)
Investment income, net .................................       444         894       4,135       8,944       5,465 
Equity in net loss of unconsolidated subsidiary ........        --          --          --      (9,028)     (4,040)
Net loss from continuing operations ....................   (27,385)    (17,292)    (22,400)    (49,670)    (50,485)
Discontinued operations ................................        --        (689)     (5,586)     (5,586)    (19,477)

Net loss ...............................................  $(27,385)   $(17,981)   $(27,986)   $(55,256)   $(69,962)
Net loss per common share from continuing operations ...  $   (.98)   $   (.57)   $   (.61)   $  (1.21)   $  (1.22)
Net loss per common share from discontinued operations .  $     --    $   (.02)   $   (.15)   $   (.14)   $   (.47)
Net loss per common share - basic and diluted ..........  $     --    $   (.59)   $   (.76)   $  (1.35)   $  (1.69)
Weighted average common shares outstanding .............    27,873      30,604      37,004      41,064      41,468 

<CAPTION>                                                                       September 30,                             
                                                                           (Amounts in thousands)                     
                                                              1994        1995        1996        1997        1998 
                                                          --------    --------   ---------    --------   ---------
<S>                                                        <C>         <C>       <C>          <C>         <C>      
BALANCE SHEET DATA:     
Working capital                                           $  8,577    $ 25,755   $ 155,246   $  82,229   $  41,417 
Total assets                                                18,278      37,516     186,438     152,930      78,197 
   
Long-term portion of notes payable                                                   
 and capital lease obligations                               1,025         782         542       1,734       1,663
    
Total liabilities                                            8,501      10,486      22,303      43,962      30,842 
Accumulated deficit                                        (60,811)    (78,792)   (106,778)   (162,034)   (231,996)
Stockholders' equity                                         9,777      21,392     144,762      96,009      39,856 
</TABLE> 


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                                   SIGNATURES


Pursuant to the requirements of the Securities Exchange Act of 1934, the 
registrant has duly caused this report to be signed on its behalf by the 
undersigned hereunto duly authorized.



                                               INTERNEURON PHARMACEUTICALS, INC.


                                               /s/ Glenn L. Cooper
                                               ---------------------------------
                                               Glenn L. Cooper, M.D.
                                                  President and Chief Executive
                                                  Officer





Dated: January 12, 1999